We appreciate your interest in studying and working at the Institute of Experimental Medicine of the Czech Academy of Sciences.

We are giving importance to the selection of new students and staff because we realize that our success and the great results of our research depend on the skills and experience of everyone. In addition, we realize that the right choice of study and employment is one of the most important decisions in our lives.

We are looking for ambitious, well-motivated, and talented students, who are interested in science. If you have the passion to make new discoveries, the drive to test new theories, and the willingness to go above and beyond, then you are just what we are looking for:)

We believe that your experience and knowledge will benefit our entire team.

We are looking forward to hearing from you! Please complete the application form. You can apply for up to 3 PhD positions.

Application deadline: 20 March, 2022

Application form

Thank you for your interest in our PhD positions, but PhD recruitment 2022 is over. We look forward to your applications next year.

PhD positions

The role of inhibitory GABAb receptors in the auditory pathways, and age-related hearing loss

Department of Auditory Neuroscience

The gamma-aminobutyric acid type B receptor (GABAb) is a G-protein coupled receptor for GABA, a major inhibitory transmitter in the mammalian nervous system. Neurons of the auditory pathway generally show high levels of GABAb expression, yet the role of these receptors in the mechanisms of auditory function is not well understood. Since changes in inhibition have been found to be associated with various forms of hearing loss, GABAb dysfunction is also expected to play a role in some pathologies of the auditory system. The aim of the project is to reveal the action of GABAb receptors in the neural circuits of subcortical and cortical auditory areas of adult and aging mammals. Experimental work will include advanced in vivo and in vitro electrophysiological methods, in vivo Ca2+ imaging using two-photon microscopy, and immunohistochemical and behavioral techniques applied to mouse models of hearing disorders such as presbycusis and tinnitus. After learning the basics of these techniques, we expect the candidate to specialize in a chosen method.

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Molecular and functional analysis of the nucleolus in 3D genome organization in early embryo development

Department of Cell Nucleus Plasticity

Eukaryotic genomes exhibit a complex 3D architecture, important for the correct execution of gene expression programs. Together with the nuclear periphery, the nucleolus is a major genome organizing structure. Upon fertilization, the parental genomes undergo an extensive spatial and epigenetic remodeling to establish totipotency. How the nucleolus participates in the 3D genome organization and correct execution of the developmental program is unknown. The aim of the project is to determine the role of embryonic nucleoli in early development using a synergistic multi-omics approach with focus on the novel Nucleolar-DamID technology to identify and functionally characterize parental genomic domains contacting the nucleolus in embryos. By artificially tethering specific sequences to nucleoli using a CRISPR/Cas9-based system, we will determine the molecular and functional contribution of nucleoli to 3D genome organization in development. The results will widen our molecular understanding of early development and provide information of high medical relevance, especially for reproductive medicine. The project will be conducted in collaboration with the University of Zurich, Switzerland.

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The role of TRPV4 and AQP4 channels in ischemic brain injury and subsequent regeneration

Department of Cellular Neurophysiology

TRPV4 nonselective cation channels are members of the TRP (transient receptor potential) channel superfamily, and are broadly expressed throughout the nervous system in neurons and several glia subpopulations, including astrocytes, NG2 glia and microglia. Due to this broad expression and their different methods of activation, TRPV4 channels are involved in numerous physiological and pathological processes. They are also suspected of cooperation with other channels found on cellular membranes, such as Aquaporin 4 (AQP4). The aim of the project will be to characterize cell-type-specific roles of TRPV4 and AQP4 channels in pathological processes, and to evaluate the influence of these channels on ischemic brain injury and regenerative processes. To achieve these aims, laboratory techniques, such as immunofluorescence, patch-clamp, fluorescence-activated cell sorting, and RNA-Seq analysis will be performed on specimens isolated from control and conditional Trpv4 and AQP4 knockout mice.

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Molecular interactions of nerve-associated cells with dermal placodes

Department of Developmental Biology

The project will study the interactions of neural crest-derived cranial nerves with epithelial structures, such as developing teeth, hair or salivary glands. We aim to reveal signals from cranial nerves and nerve-associated cells that initiate the formation of epithelial placodes corresponding to the mentioned organs. The experiments are carried out in transgenic mouse models based on tissue-specific gene inactivation in the neural crest. All required mouse strains are already available in our lab and preliminary tests have been initiated.

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Delineating the mechanisms that regulate NMDA receptors in mammalian neurons

Department of Neurochemistry

N-methyl-D-aspartate receptors (NMDARs) are a subclass of glutamate ion channels that play a critical role in excitatory neurotransmission in the mammalian brain. For this PhD project, you will study the molecular mechanisms that i) regulate the early transport of NMDARs from the endoplasmic reticulum to the neuronal surface, and ii) regulate the surface mobility and synaptic localization of individual NMDAR subtypes. To do this, you will combine advanced molecular biology approaches including lentiviral preparation, biochemistry including Western blotting and co-immunoprecipitation, live microscopy including quantum dot tracking of NMDARs, super-resolution microscopy approaches including dSTORM and SIM combined with nanobodies, and electrophysiology in autaptic hippocampal neurons from unique knock-out mouse models.

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The development of novel pharmacological compounds acting on NMDA receptors

Department of Neurochemistry

N-methyl-D-aspartate (NMDA) receptors belong to a family of ionotropic glutamate receptors that play a key role in excitatory neurotransmission in the mammalian central nervous system. Alternatively, their dysfunction leads to many neuropathological disorders including neurodegenerative diseases and cognitive deficits. In collaboration with the Biomedical Research Center in Hradec Kralove and the National Institute of Mental Health in Klecany, we will develop a series of compounds based on tacrine and MK-801 that modulate NMDA receptor activity by a unique mechanism. In this PhD project, you will investigate the molecular mechanisms of the modulatory effect of the novel compounds on NMDA receptors, using sophisticated molecular biological and electrophysiological approaches including, for example, whole-cell and single-channel measurements on transfected HEK293 cells, as well as synaptic measurements on autaptic hippocampal neurons infected with lentiviruses expressing mutated GluN subunits. Our goal is to optimize the physicochemical properties of the novel compounds, including their solubility, blood-brain barrier permeability, affinity and rate of action on individual NMDA receptor subtypes, but to minimize their side effects in vivo.

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The role of sulfation epitopes of brain extracellular matrix in aging and neurodegeneration

Department of Neuroregeneration

This PhD project aims to understand the role of Chondroitin sulphate transferase 11 (Chst11) in brain extracellular matrix (ECM), and particularly perineuronal nets (PNNs), in aging and neurodegeneration. The project follows a Chst11 knock out study (Chst11ko) in young mice.

Chondroitin sulphate proteoglycan, sulphated at the C4 epitope (in majority by Chst11), form more rigid ECM in comparison with other epitopes. This leads to a less plastic state, with lower probability of synapse formation and decreased mobility of receptors and ion channels, especially in PNN+ neurons. A major increase of C4 sulfation is observed in aging, when it dominates over other more plastic forms. According to the latest research, this could be one of the reasons for cognitive decline in the elderly population.

Using Chst11ko mice we will monitor behavioral changes in aging or tauopathy mice, with the main focus being on short or long-term memory and cognitive flexibility. Moreover, sociability, anxiety and general locomotor function will be measured. Structures of ECM/PNNs will be monitored using biochemical and immunohistochemical analysis. The changes in synaptic connectivity and activity will be measured using several techniques such as super-resolution microscopy, electrophysiology, or proteomics.

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DNA damage and repair in carcinogenesis of solid tumors

Department of Molecular Biology of Cancer

Genome instability represents one of the leading forces driving the onset and development of cancer. It arises as a consequence of the combined effect of DNA damage and errors made by the DNA repair system. In many cancers, DNA damage tolerance and DNA repair pathways are disrupted or deregulated, which increases mutagenesis and genome instability, thereby promoting cancer progression. DNA repair also appears to play a substantial role in cancer therapy response. This project will be performed in response to several unclear and unresolved issues of the role of DNA damage and DNA repair in cancer pathogenesis. The aim of the project will be searching for potential novel biomarkers and confirmation of the validity of already existing biomarkers related to DNA damage and DNA repair, which may be associated with cancer susceptibility and the patient's clinical outcome. The biological basis of different biomarkers and their associations will be also explored. Experimental work will include advanced molecular, cytogenetic, and microscopic techniques on human (cancer) samples and cancer cell lines

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If you did not find the PhD position to suit you, we would still be pleased to receive your CV (email to petr.caletka@iem.cas.cz) so that we can inform you of any new positions that become available in the future.

Organization of the PhD studies

The study is provided by the contracting universities, including Charles University in Prague, the Czech Technical University in Prague, the University of Chemistry and Technology in Prague, and others.

The main role in planning and organizing the study is played by the supervisor from IEM CAS, in cooperation with the relevant university.

The conditions of admission and the organization of studies, are governed by the valid regulations of the particular university.

Detailed information will be provided by your Supervisor.

For general questions about PhD studies, please contact our PhD Coordinator martin.horak@iem.cas.cz

About the Institute of Experimental Medicine CAS

The Institute of Experimental Medicine (IEM CAS), is a recognized center of basic biomedical research in the Czech Republic. At present, the institute consists of 11 separate scientific departments, focusing on research in biochemistry, cell and developmental biology, pathology, molecular embryology, genetic toxicology and nanotoxicology, neurobiology, neurophysiology, neuropathology, oncology, tissue replacement, and nanomedicine.

We develop and verify analytical, diagnostic, and therapeutic methods.

The research program at IEM CAS covers current trends in the field and enables interdisciplinary approaches to solving serious issues in biomedicine. Researchers of the institute actively cooperate with a number of important national and international partners. The results of research carried out at the institute are already applied in the field of environmental protection, neuroscience, regenerative medicine, pharmacology and diagnostic methods.

You can find more information on the official website www.iem.cas.cz/en

About the Czech Academy of Sciences (CAS)

The primary mission of the Czech Academy of Sciences and its institutes is to conduct research in a broad spectrum of the natural, technical and social sciences and the humanities. This research, whether highly specialized or interdisciplinary in nature, aims to advance developments in scientific knowledge at international level, while also taking into account the specific needs of both the Czech society and the national culture. Researchers of the Academy institutes also participate in education, particularly through doctoral study programs for young researchers and also by teaching at universities. The Academy also fosters collaboration with applied research and industry. The integration of Czech science into the international context is being promoted by means of numerous joint international research projects, and through the exchange of scientists with counterpart institutions abroad.

The CAS is financed primarily from the state budget. The pattern of research funding at the Academy conforms to current international standards. In addition to basic institutional financing of the research objectives of the Academy institutes, target-oriented financing is being more widely practised to carry out research projects and grant projects, selected on the basis of public competition. The CAS was the first institution in the Czech Republic to establish its own Grant Agency which financially supports research projects selected through a peer-review procedure involving reviewers from abroad. The individual Academy institutes obtain additional financial resources by participating in national and also international research programs.

You can find more information on the official website www.avcr.cz/en